Richard Gillilan wrote:
Sorry, intended this to go out to the whole group.
Here goes again:
>
> Craig Smith wrote:
> >
> > I've installed X11 server through XDarwin. Will the installation of
> > PyMOL for OS X described on your web page work with XDarwin's
> > implementation of X11 or do I have to install Apple's version. Is
> > there any advantage in installing Apple's X11? Will Apple X11
> > installation overwrite XDarwin?
> >
>
> They have encountered some problems over in OpenDx land
> with the new X11 from Apple. I have my code running mostly,
> but I think it's important to keep in mind that this is
> a beta version. Here is a quote one of the developers forwarded
> to me. It may or may not effect PyMol (uses GLUT?). Anyhow
> here it is:
>
> >Just to let you know, Apple's X11 is beta and there are problems with
> >it and X apps. For one thing the window manager does not honor any
> >window placement and window size requests. This can really make apps
> >like DX unusable. It also is missing some of the hardware rendering
> >implementation XGL and thus DX's hardware rendering will not work.
> >The developers are aware of the problems and will hopefully be
> >addressing these before the final release is finished.
>
> Richard Gillilan
> MacCHESS, Cornell

I have installed the following:
1. Apple's X11
2. Apple Dev Tools Dec. 2002
3. Fink
Typed fink install pymol. After about 30 min. of text scrolled up my
page, I get the following fatal error:
make: *** [glut_8x13.o] Error 1
### execution of failed, exit code 2
Failed: compiling glut-3.7-3 failed
So what does this mean and how do I get around it.
Craig

Under linux does anyone else see the following? If one
loads in the 1pit.pdb from the MOLMOL data files, the
resulting structure seems to have extra bonds drawn in the
side chains. For example phe's seem to have all the opposing
carbons in the rings interconnected through the center of
the ring. Thanks in advance for any hints on what is causing
that.
Jack

I am having trouble installing pymol 0.86 using fink and Apple X11 on
Mac OS X as described by Yuriwho and WScott . Previously, I have used
Fink Commander to install GIMP and ImageMagick but I cannot get any
"unstable" packages to install. I have set Fink Commander to accept
unstable packages and some show up on the Fink Commander table but
pymol 0.86 does not appear. When I try to selfupdate-CVS (either
through Fink Commander or through Terminal commands) I get the normal
messages about selfupdates and login name, then I get the following:
rm -rf /sw/fink.tmp
mkdir -p /sw/fink.tmp
chown delveccr /sw/fink.tmp
Checking to see if we can use hard links to merge the existing tree.
Please
ignore errors on the next few lines.
touch /sw/fink/README; ln /sw/fink/README /sw/fink.tmp/README
Now logging into the CVS server. When CVS asks you for a password, just
press
return (i.e. the password is empty).
su delveccr -c 'cvs
-d:pserver:anonymous@...:/cvsroot/fink login'
cvs: Command not found.
### execution of su failed, exit code 1
Failed: Logging into the CVS server for anonymous read-only access
failed.
Any ideas? I installed AppleX11 and X11SDK first, then installed Fink
and Fink Commander. I did not have any version of Fink or Xfree86
previously installed. Thanks for any help.
Bob Del Vecchio
Robert Del Vecchio
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516)367-8314

> I've installed X11 server through XDarwin. Will the installation of
> PyMOL for OS X described on your web page work with XDarwin's
> implementation of X11 or do I have to install Apple's version. Is
> there any advantage in installing Apple's X11? Will Apple X11
> installation overwrite XDarwin?
Craig,
Fink-installed PyMOL will work with Fink's Xfree86, but you should use
Apple X11 since - as other people previously reported - is way faster.
Although you can in principle install Apple's X11on top of Fink's, this
can lead to really weird phenomena (or at least it did on my Mac; I
assume this happened since both use /usr/X11R6); besides, Fink won't
know of Apple X11 until you tell it about it.
To do so, you first need to get rid of Fink's Xfree86 installations:
sudo dpkg -r --force-depends xfree86-rootless xfree86-rootless-shlibs
xfree86-base xfree86-base-shlibs
then install Apple X11 (BOTH the user and the SDK packages) by
double-clicking on the installers and following the prompts.
Finally, tell Fink to look for it:
fink install system-xfree86
which should happily find your Apple installation and configure Fink
stuff accordingly...
Hope this helps,
ciao Luca

I've installed X11 server through XDarwin. Will the installation of
PyMOL for OS X described on your web page work with XDarwin's
implementation of X11 or do I have to install Apple's version. Is
there any advantage in installing Apple's X11? Will Apple X11
installation overwrite XDarwin?

> 0. Upgrade to 10.2.3 if you have not already done so.
On a side note, did they fix NIS compatability again after breaking it in
10.2? I dropped OS X as soon as I discovered that, since that made it
nearly useless for the environment I work in. If they got it working
again, that and the new X server would be a huge incentive to get our G4s
up and running.
----------------------------------------------------------------------------
Nathaniel Echols Programmer
nat@... Gerstein Lab
203-589-6765 Yale University
----------------------------------------------------------------------------

Hi,
I have a file which measures a bunch of distances between atoms (of the
form "distance (mol1///25/ha), (mol1///26/ha)"), and rather than having to
look at the results on the screen I'd like to have the values output
to a text file. Is it possible to do this?
Thanks,
Tara
Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta

Oh, and if you already have installed pymol with fink, you don't need
to do anything apart from installing Apple's X-windows.
William G. Scott
Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax)

> Awesome! I was hoping Apple's new release might have this impact.
In my hands the X-windows version of pymol on OS X went from unusable
to almost as fast as the native version.
>
> Apple's GLUT driver can now bind to the hardware drivers under X11 at
> the
> same time as the Tcl/Tk external GUI. It used to be an either/or
> situation. Apple has finally answered our requrests to support a fast
> 3D
> environment just like Linux and Windows, without requiring developers
> to
> specifically write to their user interface (which has taken me a lot
> of
> time, and I'm still not done)!
>
> Can you (or someone else knowledgable) please paste a quick summary for
> newbies as to how they would go about getting PyMOL running under
> Fink with the new OSX release?
0. Upgrade to 10.2.3 if you have not already done so.
1. Download X-windows from apple and install it
(more details in the blue box here:
http://chemistry.ucsc.edu/%7Ewgscott/xtal/page1.html )
currently free but once they get everyone addicted....
2. Download Apple's December 2002 developer tools and install it (this
includes compilers)
http://developer.apple.com/tools/macosxtools.html
Free but you have to register.
3. Download fink and install it (more details here:
http://chemistry.ucsc.edu/%7Ewgscott/xtal/page3.html )
4. type fink install pymol (this installs pymol and all of its
dependencies like python).
>
> Thanks.
>
> Cheers,
> Warren
William G. Scott
Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
phone: +1-831-459-5367 (office)
+1-831-459-5292 (lab)
fax: +1-831-4593139 (fax)

To get the fink 0.86 version of PyMOL running hardware accelerated on
Mac OS X using Apples newly released X11 you will need to install both
Apples X11 public beta and their X11 software development kit available
here:
http://www.apple.com/macosx/x11/
You also need to get fink up and running. Detailed instructions for
installing fink can be found here:
http://fink.sourceforge.net/doc/bundled/install.php
instructions for setting up fink to use Apples X11 XServer can be found
here:
http://fink.sourceforge.net/doc/x11/inst-xfree86.php#apple-binary
once you have installed fink and apples X11, you will need to compile
PyMOL
I would recommend that newbies use fink commander to get their fink
installation configured correctly. You need to enable the preference to
use unstable packages in the Fink Commander preferences before you
attempt to install PyMOL as the 0.86 release is not yet rated as stable
(although it works fine for me). Fink commander can be found here:
http://www.versiontracker.com/moreinfo.fcgi?id=15256&db=mac
after getting fink up and running (with selfupdate-cvs) using the
unstable tree and apples X11 all you need to do to get PyMOL 0.86
running is to type
sudo fink install pymol
in a terminal or just highlight the pymol package in Fink Commander and
select the > source >install command from the menus) this should build
PyMOL 0.86 and all required dependencies (~15 packages in all). This
will take quite a while so don't be impatient.
Finally launch Apples X11.app and under the applications menu select
customize then add an item called PyMOL with the command /sw/bin/pymol
and you should now be able to launch accelerated PyMOL from the
applications menu
Cheers and enjoy,
Y
On Wednesday, January 8, 2003, at 10:13 AM, Warren L. DeLano wrote:
>
> Awesome! I was hoping Apple's new release might have this impact.
>
> Apple's GLUT driver can now bind to the hardware drivers under X11 at
> the
> same time as the Tcl/Tk external GUI. It used to be an either/or
> situation. Apple has finally answered our requrests to support a fast
> 3D
> environment just like Linux and Windows, without requiring developers
> to
> specifically write to their user interface (which has taken me a lot
> of
> time, and I'm still not done)!
>
> Can you (or someone else knowledgable) please paste a quick summary for
> newbies as to how they would go about getting PyMOL running under
> Fink with the new OSX release?
>
> Thanks.
>
> Cheers,
> Warren
>
> On Wed, 8 Jan 2003, yuriwho wrote:
>
>> I would like to report that 0.86 works fine under MacOS X 10.2.3 using
>> Apples X11 version of xwindows. As far as I can tell it also has
>> graphics acceleration (but I'm not sure as I haven't done any rigorous
>> tests...seems dramatically faster than previous xwindows(fink)
>> versions
>> of pymol). I am using the latest fink package on a TiBook 800.
>>
>> Can anyone else comment about speed/features using 0.86 under X11
>> versus current/future MacOS X ports?
>>
>> It is nice to have the more full featured menus again.
>>
>> Y
>>
>> Yuriwho@...

Hi Dirk
This might actually be a hardware affect rather than a software effect.
The GeForce4
is undoubtably quicker that the GeForce 2 bu there comes a time when the
actual CPU is lagging behind in the amount of data it can pass to the GPU-
this also includes other limitations such as the graphics apature size
setting in the bios, the amount of RAM available to the machine and the
speed of the AGP BUS. Putting a GeForce4 into a PIII means the GPU will be
idling a lot probably upgrading the motherboard, RAM and CPU will yield
improvements, better graphics cards most likely won't.
Jules
On Wed, 8 Jan 2003, Dirk Kostrewa wrote:
> Dear Gordon,
>
> I assume that you changed the default "nv" driver in your XF86config(-4) file
> to the Nvidia driver "nvidia". I've replaced on my private Pentium III (733
> MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less
> improvement than expected. Here are my observations:
> 1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is
> probably okay.
> 2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchmark
> program "gears" in full-screen mode and somewhat less than this in the
> Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23).
> 3. But, puzzlingly with pymol and on-screen rendering of a complex secondary
> structure sketch (without ray-tracing) I only get a moderate increase (~ 10
> %, or so) of the movie frame rate compared to a Geforce2MX440 running on a
> Pentium III (450 MHz) in my office! Here, I would really expect a huge
> difference in frame rate. I also don't understand this. A possible
> explanation would be that pymol, upon automatic detection of the graphics
> card, internally changes the complexity of the calculations resulting in a
> slower but improved image?
>
> Best regards,
>
> Dirk.
>
> On Wednesday 08 January 2003 09:40, gordon wrote:
> > Hi
> > I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't
> > really notice a performance improvment (running linux). I judge this
> > based on how smoothly large sized proteins can be rotated with spheres
> > on.
> > Just wondering why?
>

Awesome! I was hoping Apple's new release might have this impact.
Apple's GLUT driver can now bind to the hardware drivers under X11 at the
same time as the Tcl/Tk external GUI. It used to be an either/or
situation. Apple has finally answered our requrests to support a fast 3D
environment just like Linux and Windows, without requiring developers to
specifically write to their user interface (which has taken me a lot of
time, and I'm still not done)!
Can you (or someone else knowledgable) please paste a quick summary for
newbies as to how they would go about getting PyMOL running under
Fink with the new OSX release?
Thanks.
Cheers,
Warren
On Wed, 8 Jan 2003, yuriwho wrote:
> I would like to report that 0.86 works fine under MacOS X 10.2.3 using
> Apples X11 version of xwindows. As far as I can tell it also has
> graphics acceleration (but I'm not sure as I haven't done any rigorous
> tests...seems dramatically faster than previous xwindows(fink) versions
> of pymol). I am using the latest fink package on a TiBook 800.
>
> Can anyone else comment about speed/features using 0.86 under X11
> versus current/future MacOS X ports?
>
> It is nice to have the more full featured menus again.
>
> Y
>
> Yuriwho@...
>
>
>
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Many thanks for the replies. I had forgotten the import statement (Doh!).
Now working fine again.
On a different note, one of the best features of 0.86, in my humble
opinion, is the new scrolling objects list. Previously I've created
sidechain objects to toggle individual sidechains on/off with one mouse
click using the following:
create MET1, (1/* & !n;N,C,O,H,HA,H03)
cmd.show("sticks","MET1")
util.cbaw("MET1")
cmd.disable('MET1') # disable at startup
and for small proteins it's not too time consuming to cut/paste/alter a
script to do this for every sidechain in the molecule (performance is a tad
slow on my old PII/NT machine but fine on faster PCs). Now I can toggle any
sidechain on/off with one mouse click and it doesn't matter how many
objects I have, similar to what you can do in SwissPDB viewer.
Any way my question is, can anybody think of a way to write a script that
would iterate through any pdb file and create individual objects MET1,
ALA2, ASP3... to AAn etc at the push of a scriptbox button?? My
python/scripting isn't so good but I'm learning!
Cheers,
Chris.
___________________________________________________________
Dr Chris Winfield Lab: N317/318
Post-Doctoral Researcher Tel: +44 (0)1179 546 324
School of Chemistry Fax: +44 (0)1179 298 611
University of Bristol Mob: +44 (0)7866 550 518
Cantocks Close chris.winfield@...
Bristol BS8 1TS
___________________________________________________________
--On 08 January 2003 12:24 +0100 Kristian Rother
<kristian.rother@...> wrote:
> Am Dienstag, 7. Januar 2003 11:08 schrieb Chris Winfield:
>> Has anybody managed to get ScriptBox working under Windows with v0.86??
>
> Yes, me at least :-)
>
>> I'm
>> having trouble.
>
> Here's my checklist:
>
> 1.) Did you write an 'import ScriptBox' statement into PMGApp.py?
>
> 2.) Is Scriptbox.py really in the pmg_tk directory (OK, You mentioned
> that already)?
>
> Hm, the people i know of had no problems further than this yet. Let me
> know whether this works.
>
> Kristian
>
>>
>> I put ScriptBox.py in the appropriate placeplace and the following at the
>> end of the createMain(self) procedure in PMGApp.py in the usual manner:
>>
>> ScriptBox.__init__(self)
>>
>> But get the following error on loading PyMol:
>>
>> NameError: global name 'ScriptBox' is not defined
>>
>> If anyone has any suggestions they'd be most appreciated. I like
>> ScriptBox a lot so do you think there's any chance of incorporating this
>> into PyMol either as a GUI window or as its own dropdown scripts menu
>> that could also list all the scripts in a given directory??
>>
>> Cheers,
>>
>> Chris.
>> ___________________________________________________________
>>
>> Dr Chris Winfield Lab: N317/318
>> Post-Doctoral Researcher Tel: +44 (0)1179 546 324
>> School of Chemistry Fax: +44 (0)1179 298 611
>> University of Bristol Mob: +44 (0)7866 550 518
>> Cantocks Close chris.winfield@...
>> Bristol BS8 1TS
>> ___________________________________________________________
>>
>>
>>
>> -------------------------------------------------------
>> This SF.NET email is sponsored by:
>> SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See!
>> http://www.vasoftware.com
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Dear Gordon,
I assume that you changed the default "nv" driver in your XF86config(-4) =
file=20
to the Nvidia driver "nvidia". I've replaced on my private Pentium III (7=
33=20
MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less=20
improvement than expected. Here are my observations:
1. Under Windows98SE with 3DMark2001 I get a ~50 % higher score, which is=
=20
probably okay.
2. Under Linux I get a ~ doubled frame rate for the simple OpenGL benchma=
rk=20
program "gears" in full-screen mode and somewhat less than this in the=20
Vulpine OpenGL Mark, which is fine (Nvidia driver 31.23).
3. But, puzzlingly with pymol and on-screen rendering of a complex second=
ary=20
structure sketch (without ray-tracing) I only get a moderate increase (~ =
10=20
%, or so) of the movie frame rate compared to a Geforce2MX440 running on =
a=20
Pentium III (450 MHz) in my office! Here, I would really expect a huge=20
difference in frame rate. I also don't understand this. A possible=20
explanation would be that pymol, upon automatic detection of the graphics=
=20
card, internally changes the complexity of the calculations resulting in =
a=20
slower but improved image?
Best regards,
Dirk.
On Wednesday 08 January 2003 09:40, gordon wrote:
> Hi
> I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't
> really notice a performance improvment (running linux). I judge this
> based on how smoothly large sized proteins can be rotated with spheres
> on.
> Just wondering why?
>
> Thanks in advance
> Gordon
--=20
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OSRA/007
CH-5232 Villigen PSI, Switzerland
E-mail: dirk.kostrewa@...
Phone: +41-56-310-4722
Fax: +41-56-310-4556
WWW: http://www.sb.psi.ch
****************************************

> If anyone has any suggestions they'd be most appreciated. I like Script=
Box
> a lot so do you think there's any chance of incorporating this into PyM=
ol
> either as a GUI window or as its own dropdown scripts menu that could a=
lso
> list all the scripts in a given directory??
Hello,
There is a very recent (6.1.) package of rTools available from=20
http://www.rubor.de/bioinf , where ScriptBox and some other tools are=20
contained. Most things are accessible from menus, You can also add Your o=
wn=20
scripts to the box using the add_script command.
rTools 0.5.2 is still a Beta release, although many bugs have been fixed=20
already. Particularly, installation under Windows is still a little=20
eXPerience.
Kristian Rother

Hi
I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't
really notice a performance improvment (running linux). I judge this
based on how smoothly large sized proteins can be rotated with spheres
on.
Just wondering why?
Thanks in advance
Gordon
--
Gordon Wells
Department of Biochemistry
University of Pretoria

I would like to report that 0.86 works fine under MacOS X 10.2.3 using
Apples X11 version of xwindows. As far as I can tell it also has
graphics acceleration (but I'm not sure as I haven't done any rigorous
tests...seems dramatically faster than previous xwindows(fink) versions
of pymol). I am using the latest fink package on a TiBook 800.
Can anyone else comment about speed/features using 0.86 under X11
versus current/future MacOS X ports?
It is nice to have the more full featured menus again.
Y
Yuriwho@...

Stephen,
You're looking for the PyMOL API function "extend":
from pymol import cmd
cmd.extend("ramp_colors",ramp_chain.ramp_colors)
Would then permit the following:
ramp_colors chain A
See "help extend" for more info...
Cheers,
Warren
--
mailto:warren@...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501
> -----Original Message-----
> From: Stephen Graham [mailto:stepheng@...]
> Sent: Tuesday, January 07, 2003 4:14 PM
> To: pymol-users@...
> Subject: [PyMOL] "Rolling your own" functions in PyMol
>=20
>=20
> Hi All,
>=20
> I am a recent subscriber to the list, so apologies if this=20
> question has
> been answered before. I am interested in finding out how you can add
> your own functions to PyMol such that they may be=20
> "transparently" called
> from inside PyMol's shell. The the basic question is "How do=20
> I register
> PyMol names for home-grown functions so that they can be used like the
> functions in the util module". A more detailed example of what I am
> after is below. Also, are there any warehouses or collections of
> home-grown functions to which I could submit functions I=20
> write and from
> which I could gain examples from other users?
>=20
> Cheers
>=20
> Stephen
>=20
> =3D=3D More detailed description of my problem =3D=3D
>=20
> I have written a function to ramp coloring of a backbone=20
> between two or
> more arbitrary colors (it is really a generalization of the code in
> util.rainbow). I have imported the code using the general=20
> Python import
> command:
> import ramp_chain
> Now, let's say that I have a selection object defined as:
> select A,(chain A)
> Were I using the rainbow command I would be able to issue the command:
> util.rainbow A
> Which follows the general rules of command line parsing. =20
> Unfortunately,
> in my case issuing the command:
> ramp_chain.ramp_colors A
> gives the error:
> Syntax error: unexpected EOF (and there is an arrow under the letter
> A).
> I *can* call the command using the syntax:
> ramp_chain.ramp_colors( "chain A" )
> but this syntax is not optimal - I would like to be able to use my
> already defined selections.
>=20
> --=20
> Stephen Graham
> PhD candidate and nasty sysadmin
> Crystallography Group
> School of Molecular and Microbial Biosciences
> Building G08
> University of Sydney
> New South Wales, 2006
> Australia
> Ph: +61 2 9351 8197
> Fax: +61 2 9351 4726
>=20
>=20
> -------------------------------------------------------
> This SF.NET email is sponsored by:
> SourceForge Enterprise Edition + IBM + LinuxWorld =3D Something 2 See!
> http://www.vasoftware.com
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hi All,
I am a recent subscriber to the list, so apologies if this question has
been answered before. I am interested in finding out how you can add
your own functions to PyMol such that they may be "transparently" called
from inside PyMol's shell. The the basic question is "How do I register
PyMol names for home-grown functions so that they can be used like the
functions in the util module". A more detailed example of what I am
after is below. Also, are there any warehouses or collections of
home-grown functions to which I could submit functions I write and from
which I could gain examples from other users?
Cheers
Stephen
== More detailed description of my problem ==
I have written a function to ramp coloring of a backbone between two or
more arbitrary colors (it is really a generalization of the code in
util.rainbow). I have imported the code using the general Python import
command:
import ramp_chain
Now, let's say that I have a selection object defined as:
select A,(chain A)
Were I using the rainbow command I would be able to issue the command:
util.rainbow A
Which follows the general rules of command line parsing. Unfortunately,
in my case issuing the command:
ramp_chain.ramp_colors A
gives the error:
Syntax error: unexpected EOF (and there is an arrow under the letter
A).
I *can* call the command using the syntax:
ramp_chain.ramp_colors( "chain A" )
but this syntax is not optimal - I would like to be able to use my
already defined selections.
--
Stephen Graham
PhD candidate and nasty sysadmin
Crystallography Group
School of Molecular and Microbial Biosciences
Building G08
University of Sydney
New South Wales, 2006
Australia
Ph: +61 2 9351 8197
Fax: +61 2 9351 4726

Has anybody managed to get ScriptBox working under Windows with v0.86?? I'm
having trouble.
I put ScriptBox.py in the appropriate placeplace and the following at the
end of the createMain(self) procedure in PMGApp.py in the usual manner:
ScriptBox.__init__(self)
But get the following error on loading PyMol:
NameError: global name 'ScriptBox' is not defined
If anyone has any suggestions they'd be most appreciated. I like ScriptBox
a lot so do you think there's any chance of incorporating this into PyMol
either as a GUI window or as its own dropdown scripts menu that could also
list all the scripts in a given directory??
Cheers,
Chris.
___________________________________________________________
Dr Chris Winfield Lab: N317/318
Post-Doctoral Researcher Tel: +44 (0)1179 546 324
School of Chemistry Fax: +44 (0)1179 298 611
University of Bristol Mob: +44 (0)7866 550 518
Cantocks Close chris.winfield@...
Bristol BS8 1TS
___________________________________________________________

A new PyMOL version has been released. There is only one major feature
addition, but it makes a huge difference in the user experience. It is:
SESSION SAVES!
You can now save and restore PyMOL's state instead of having to write
laborious scripts. Hopefully this will make PyMOL more accessible to
non-programmers.
PyMOL session files have a ".pse" extension. You can save or load them
using the command line or the File menu.
Other changes include:
- Command history in external gui (use up/down arrows).
- Shadows can be disabled ("set ray_shadows,0").
- A scroll bar appears for long lists of object names.
- You can now adjust the width of the internal gui using the mouse.
- Reorganized menus.
- Amber trajectory file support (requires matched .top and .trj files
-- read "help load_traj")
- A few textures for the raytracer.
- Better support for Python blocks in PyMOL command scripts.
- "center" command
...and a variety of other minor tweaks.
Please let me know ASAP if there are any problems with the file releases.
Thanks,
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
PS. Sorry no OSX release right now. Soon hopefully!

Community

Help

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:

CountryState

JavaScript is required for this form.

I agree to receive quotes, newsletters and other information from sourceforge.net and its partners regarding IT services and products. I understand that I can withdraw my consent at any time. Please refer to our Privacy Policy or Contact Us for more details